This article is from the Watercooled VWs General FAQ, by Jan Vandenbrande with numerous contributions by others.
A: They all do that. According to Jens Knickmeyer:
This problem is well known at VW. The reason is the gear-box. The tooth
wheels (a pair for each gear) have too much space between the teeth
which results in the rattle. Nothing to worry about, there are other
cars with the same symptom (Polo-G40, Audi 100, VW LT28, ...)
Some reported similar problems with a heat shield ratteling
but in that case the sound will be independent of whether you
push the clutch in.
 
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